[gmx-users] Position restraint coordinates are missing

[Justin Lemkul]

On 4/8/14, 8:44 PM, Yujie Wang wrote:
> Hi, gromacs users
>
>     I have some qestions about the tpr files, I want to extract the energy of
> subset via
>
>       tpbconv -f all.tpr -n index.ndx -nsteps -1  -o subset.tpr
>       mdrun -rerun subset.trr -s subset.tpr
>
>      where the subset atom was defined in index file. I obtain the following
> error:
>
>        Software inconsistency error:
>       Position restraint coordinates are missing
>
>      the atom of subset did not be confined. I just confined some other
> atoms.
>      what should I do ?  Any suggestion is appreciated. Thank you very much!
>

Create a new .tpr file that has no position restraints in it, then extract the 
atoms you want with tpbconv and proceed to mdrun -rerun.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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